forked from lijiext/lammps
155 lines
5.6 KiB
Plaintext
155 lines
5.6 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style lj/sdk command :h3
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pair_style lj/sdk/gpu command :h3
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pair_style lj/sdk/omp command :h3
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pair_style lj/sdk/coul/long command :h3
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pair_style lj/sdk/coul/long/gpu command :h3
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pair_style lj/sdk/coul/long/omp command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/sdk} or {lj/sdk/coul/long}
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args = list of arguments for a particular style :ul
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{lj/sdk} args = cutoff
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cutoff = global cutoff for Lennard Jones interactions (distance units)
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{lj/sdk/coul/long} args = cutoff (cutoff2)
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cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
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[Examples:]
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pair_style lj/sdk 2.5
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pair_coeff 1 1 lj12_6 1 1.1 2.8 :pre
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pair_style lj/sdk/coul/long 10.0
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pair_style lj/sdk/coul/long 10.0 12.0
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pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
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[Description:]
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The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
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given by
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:c,image(Eqs/pair_cmm.jpg)
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as required for the SDK Coarse-grained MD parametrization discussed in
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"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff.
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Style {lj/sdk/coul/long} computes the adds Coulombic interactions
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with an additional damping factor applied so it can be used in
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conjunction with the "kspace_style"_kspace_style.html command and
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its {ewald} or {pppm} or {pppm/cg} option. The Coulombic cutoff
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specified for this style means that pairwise interactions within
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this distance are computed directly; interactions outside that
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distance are computed in reciprocal space.
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The following coefficients must be defined for each pair of atoms
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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cg_type (lj9_6, lj12_4, or lj12_6)
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epsilon (energy units)
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sigma (distance units)
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cutoff1 (distance units) :ul
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum. The prefactors
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are chosen so that the potential minimum is at -epsilon.
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The latter 2 coefficients are optional. If not specified, the global
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LJ and Coulombic cutoffs specified in the pair_style command are used.
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If only one cutoff is specified, it is used as the cutoff for both LJ
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and Coulombic interactions for this type pair. If both coefficients
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are specified, they are used as the LJ and Coulombic cutoffs for this
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type pair.
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For {lj/sdk/coul/long} only the LJ cutoff can be specified since a
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Coulombic cutoff cannot be specified for an individual I,J type pair.
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All type pairs use the same global Coulombic cutoff specified in the
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pair_style command.
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:line
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Styles with a {cuda}, {gpu}, {omp} or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-OMP, and
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OPT packages respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Mixing, shift, table, tail correction, restart, and rRESPA info]:
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For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the lj/sdk pair styles {cannot} be mixed,
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since different pairs may have different exponents. So all parameters
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for all pairs have to be specified explicitly through the "pair_coeff"
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command. Defining then in a data file is also not supported, due to
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limitations of that file format.
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All of the lj/sdk pair styles support the
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"pair_modify"_pair_modify.html shift option for the energy of the
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Lennard-Jones portion of the pair interaction.
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The {lj/sdk/coul/long} pair styles support the
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"pair_modify"_pair_modify.html table option since they can tabulate
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the short-range portion of the long-range Coulombic interaction.
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All of the lj/sdk pair styles write their information to "binary
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restart files"_restart.html, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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The lj/sdk and lj/cut/coul/long pair styles do not support
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the use of the {inner}, {middle}, and {outer} keywords of the "run_style
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respa"_run_style.html command.
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:line
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[Restrictions:]
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All of the lj/sdk pair styles are part of the USER-CG-CMM package.
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The {lj/sdk/coul/long} style also requires the KSPACE package to be
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built (which is enabled by default). They are only enabled if LAMMPS
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was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html, "angle_style sdk"_angle_sdk.html
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[Default:] none
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:line
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:link(Shinoda)
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[(Shinoda)] Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
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:link(DeVane)
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[(DeVane)] Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
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